Hi Atomriot,
maybe you already solved this problem?
if not, I think the problem is related to the power feeding the Rainbowduino:
when the power is not enough, like if you power the board just from the UartUsb,
only the red LED will light, while the green and blue stay almost dark.
Try using a transformer capable of at least 500mA (better 1A), at 6V to keep the baby cool and chilled;
sometimes I used 12V but after a while the matrix got quite hot!
Hope this helps,
all the best,
kk